colvar::h_bond Class Reference

Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]). More...

#include <colvarcomp.h>

Inheritance diagram for colvar::h_bond:

List of all members.

Public Member Functions
	h_bond (std::string const &conf)
	h_bond (cvm::atom const &acceptor, cvm::atom const &donor, cvm::real r0, int en, int ed)
	Constructor for atoms already allocated.
	h_bond ()
virtual	~h_bond ()
virtual void	calc_value ()
	Calculate the variable.
virtual void	calc_gradients ()
	Calculate the atomic gradients, to be reused later in order to apply forces.
virtual void	apply_force (colvarvalue const &force)
	Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function).
virtual cvm::real	dist2 (colvarvalue const &x1, colvarvalue const &x2) const
	Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_lgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual colvarvalue	dist2_rgrad (colvarvalue const &x1, colvarvalue const &x2) const
	Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities).
virtual cvm::real	compare (colvarvalue const &x1, colvarvalue const &x2) const
	Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error.
Protected Attributes
cvm::atom	acceptor
	Atoms involved in the component.
cvm::atom	donor
	Atoms involved in the component.
cvm::real	r0
	"Cutoff" distance between acceptor and donor
int	en
	Integer exponent of the function numerator.
int	ed
	Integer exponent of the function denominator.

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Detailed Description

Colvar component: hydrogen bond, defined as the product of a colvar::coordnum and 1/2*(1-cos((180-ang)/ang_tol)) (colvarvalue::type_scalar type, range [0:1]).

Definition at line 707 of file colvarcomp.h.

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Constructor & Destructor Documentation

colvar::h_bond::h_bond (  std::string const &  conf  )

Definition at line 218 of file colvarcomp_coordnums.C. References acceptor, colvarmodule::atom, donor, ed, en, colvarmodule::fatal_error(), r0, and colvarvalue::type(). : cvc (conf) { function_type = "h_bond"; x.type (colvarvalue::type_scalar); int a_num, d_num; get_keyval (conf, "acceptor", a_num, -1); get_keyval (conf, "donor", d_num, -1); if ( (a_num == -1) || (d_num == -1) ) { cvm::fatal_error ("Error: either acceptor or donor undefined.\n"); } acceptor = cvm::atom (a_num); donor = cvm::atom (d_num); get_keyval (conf, "cutoff", r0, (3.3 * cvm::unit_angstrom())); get_keyval (conf, "expNumer", en, 6); get_keyval (conf, "expDenom", ed, 8); if ( (en%2) || (ed%2) ) { cvm::fatal_error ("Error: odd exponents provided, can only use even ones.\n"); } }

colvar::h_bond::h_bond (  cvm::atom const &  acceptor, cvm::atom const &  donor, cvm::real  r0, int  en, int  ed )

Constructor for atoms already allocated. Definition at line 245 of file colvarcomp_coordnums.C. References colvarvalue::type(). : acceptor (acceptor_i), donor (donor_i), r0 (r0_i), en (en_i), ed (ed_i) { function_type = "h_bond"; x.type (colvarvalue::type_scalar); }

colvar::h_bond::h_bond (   )

Definition at line 257 of file colvarcomp_coordnums.C. References colvarvalue::type(). : cvc () { function_type = "h_bond"; x.type (colvarvalue::type_scalar); }

virtual colvar::h_bond::~h_bond (   )  [inline, virtual]

Definition at line 726 of file colvarcomp.h. {}

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Member Function Documentation

void colvar::h_bond::apply_force (  colvarvalue const &  force  )  [virtual]

Apply the collective variable force, by communicating the atomic forces to the simulation program (Note: the member is not altered by this function). Note: multiple calls to this function within the same simulation step will add the forces altogether Parameters: cvforce  The collective variable force, usually coming from the biases and eventually manipulated by the parent object Implements colvar::cvc. Definition at line 286 of file colvarcomp_coordnums.C. References acceptor, colvarmodule::atom::apply_force(), donor, colvarmodule::atom::grad, and colvarvalue::real_value. { acceptor.apply_force (force.real_value * acceptor.grad); donor.apply_force (force.real_value * donor.grad); }

void colvar::h_bond::calc_gradients (   )  [virtual]

Calculate the atomic gradients, to be reused later in order to apply forces. Implements colvar::cvc. Definition at line 280 of file colvarcomp_coordnums.C. { colvar::coordnum::switching_function<true> (r0, en, ed, acceptor, donor); }

void colvar::h_bond::calc_value (   )  [virtual]

Calculate the variable. Implements colvar::cvc. Definition at line 266 of file colvarcomp_coordnums.C. References acceptor, donor, colvarmodule::atom::read_position(), colvarvalue::real_value, and colvarmodule::atom::reset_data(). { // this is necessary, because switching_function() will sum the new // gradient to the current one acceptor.reset_data(); donor.reset_data(); acceptor.read_position(); donor.read_position(); x.real_value = colvar::coordnum::switching_function<false> (r0, en, ed, acceptor, donor); }

virtual cvm::real colvar::h_bond::compare (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Return a positive number if x2>x1, zero if x2==x1, negative otherwise (can be redefined to transparently implement constraints, symmetries and periodicities) Note: it only works with scalar variables, otherwise raises an error. Reimplemented from colvar::cvc.

virtual cvm::real colvar::h_bond::dist2 (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Square distance between x1 and x2 (can be redefined to transparently implement constraints, symmetries and periodicities). colvar::cvc::dist2() and the related functions are declared as "const" functions, but not "static", because additional parameters defining the metrics (e.g. the periodicity) may be specific to each colvar::cvc object. If symmetries or periodicities are present, the colvar::cvc::dist2() should be redefined to return the "closest distance" value and colvar::cvc::dist2_lgrad(), colvar::cvc::dist2_rgrad() to return its gradients. If constraints are present (and not already implemented by any of the types), the colvar::cvc::dist2_lgrad() and colvar::cvc::dist2_rgrad() functions should be redefined to provide a gradient which is compatible with the constraint, i.e. already deprived of its component normal to the constraint hypersurface. Finally, another useful application, if you are performing very many operations with these functions, could be to override the member functions and access directly its member data. For instance: to define dist2(x1,x2) as (x2.real_value-x1.real_value)*(x2.real_value-x1.real_value) in case of a scalar type. Reimplemented from colvar::cvc.

virtual colvarvalue colvar::h_bond::dist2_lgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Gradient (with respect to x1) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::cvc.

virtual colvarvalue colvar::h_bond::dist2_rgrad (  colvarvalue const &  x1, colvarvalue const &  x2 )  const [virtual]

Gradient (with respect to x2) of the square distance (can be redefined to transparently implement constraints, symmetries and periodicities). Reimplemented from colvar::cvc.

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Member Data Documentation

cvm::atom colvar::h_bond::acceptor [protected]

Atoms involved in the component. Definition at line 712 of file colvarcomp.h. Referenced by apply_force(), calc_value(), and h_bond().

cvm::atom colvar::h_bond::donor [protected]

Atoms involved in the component. Definition at line 712 of file colvarcomp.h. Referenced by apply_force(), calc_value(), and h_bond().

int colvar::h_bond::ed [protected]

Integer exponent of the function denominator. Definition at line 718 of file colvarcomp.h. Referenced by h_bond().

int colvar::h_bond::en [protected]

Integer exponent of the function numerator. Definition at line 716 of file colvarcomp.h. Referenced by h_bond().

cvm::real colvar::h_bond::r0 [protected]

"Cutoff" distance between acceptor and donor Definition at line 714 of file colvarcomp.h. Referenced by h_bond().

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The documentation for this class was generated from the following files:

• colvarcomp.h
• colvarcomp_coordnums.C

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